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P SS, Chennuru S, Krovvidi S, Chitichoti J. Status of tick-borne haemoprotozoan infection in south Indian sheep in association with variation in Ovar-DRB1 gene. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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2
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Hassan SU, Chua EG, Paz EA, Kaur P, Tay CY, Greeff JC, Liu S, Martin GB. Investigating the development of diarrhoea through gene expression analysis in sheep genetically resistant to gastrointestinal helminth infection. Sci Rep 2022; 12:2207. [PMID: 35140270 PMCID: PMC8828848 DOI: 10.1038/s41598-022-06001-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Gastrointestinal helminths infect livestock causing health problems including severe diarrhoea. To explore the underlying biological mechanisms relating to development and control of diarrhoea, we compared 4 sheep that were susceptible to development of diarrhoea with 4 sheep that were diarrhoea-resistant. Transcriptomes in the tissues where the parasites were located were analyzed using RNASeq. By considering low-diarrhoea sheep as control, we identified 114 genes that were down-regulated and 552 genes that were up-regulated genes in the high-diarrhoea phenotype. Functional analysis of DEGs and PPI sub-network analysis showed that down-regulated genes in the high-diarrhoea phenotype were linked to biological processes and pathways that include suppression of ‘antigen processing and presentation’, ‘immune response’, and a list of biological functional terms related to ‘suppression in immune tolerance’. On the other hand, up-regulated genes in the high-diarrhoea phenotype probably contribute to repair processes associated with tissue damage, including ‘extracellular matrix organization’, ‘collagen fibril organization’, ‘tissue morphogenesis’, ‘circulatory system development’, ‘morphogenesis of an epithelium’, and ‘focal adhesion’. The genes with important roles in the responses to helminth infection could be targeted in breeding programs to prevent diarrhoea.
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Affiliation(s)
- Shamshad Ul Hassan
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia.,Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Eng Guan Chua
- Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Erwin A Paz
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia.,Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Chin Yen Tay
- Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Johan C Greeff
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia.,Department of Primary Industries and Regional Development, Western Australia, 3 Baron Hay Court, South Perth, WA, 6151, Australia
| | - Shimin Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Graeme B Martin
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia.
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Esmailnejad A, Ganjiani V, Hosseini-Nasab E, Nazifi S. Association of Ovar-DRB1 alleles with innate immune responses in sheep. Vet Med Sci 2021; 8:752-757. [PMID: 34882990 PMCID: PMC8959254 DOI: 10.1002/vms3.683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Major histocompatibility complex (MHC) is the best characterised genetic region associated with adaptive immune responses, including humoral and cell‐mediated immunities. Objectives In this study, the association of MHC class II alleles with inflammatory cytokines and acute‐phase proteins was evaluated in sheep population. Methods Allelic diversity of second exon of ovine DRB1 locus (Ovar‐DRB1.2) was determined in 100 indigenous Iranian Lori‐Bakhtiari fat‐tailed sheep using restriction fragment length polymorphism and direct sequencing methods. The association of DRB1.2 alleles with inflammatory cytokines (interleukin‐1β, IL‐1β; IL‐6 and tumour necrosis factor‐α) and acute‐phase proteins (serum amyloid A, alpha‐1‐acid glycoprotein and haptoglobin) was examined using generalised linear model and multivariate regression analysis. Results Seven distinct RsaI restriction patterns and fourteen alleles were identified in this population. Allele DRB1*2101 showed a negative influence on the IL‐6 response and was associated with lower serum level of IL‐6. DRB1.2 heterozygous individuals also showed higher haptoglobin concentration than homozygotes. Conclusions These results provide additional support for the association between Ovar‐DRB1 alleles and regulation of immune responses in sheep population. Description of MHC polymorphism and its role in the controlling of immune responses will increase our understanding of host–pathogen interactions, and ultimately facilitate the selection of disease‐resistant flocks in genetic breeding programs.
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Affiliation(s)
- Atefeh Esmailnejad
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Vahid Ganjiani
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | | | - Saeed Nazifi
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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Yaman Y, Bay V, Aymaz R, Keleş M, Öner Y, Teferedegn EY, Ün C. A novel 2 bp deletion variant in Ovine-DRB1 gene is associated with increased Visna/maedi susceptibility in Turkish sheep. Sci Rep 2021; 11:14435. [PMID: 34262107 PMCID: PMC8280167 DOI: 10.1038/s41598-021-93864-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
Visna/maedi (VM) is a multisystemic lentivirus infection of sheep that affecting sheep industry across the globe. TMEM154 gene has been identified to be a major VM-associated host gene, nevertheless, a recent study showed that the frequency of the VM-resistant TMEM154 haplotypes was very low or absent in indigenous sheep. Thus, the present study was designed to determine other possible co-receptors associated with VM. For this purpose, DRB1 gene, which is renowned for its role in host immune response against various diseases was targeted. A total number of 151 case-control matched pairs were constructed from 2266 serologically tested sheep. A broad range of DRB1 haplotype diversity was detected by sequence-based genotyping. Moreover, a novel 2 bp deletion (del) in the DRB1 intron 1 was identified. For the final statistic, the sheep carrying VM-resistant TMEM154 diplotypes were removed and a McNemar's test with a matched pairs experimental design was conducted. Consequently, it was identified for the first time that the 2 bp del variant is a genetic risk factor for VM (p value 0.002; chi-square 8.31; odds ratio 2.9; statistical power 0.90) in the dominant model. Thus, negative selection for 2 bp del variant could decrease VM infection risk in Turkish sheep.
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Affiliation(s)
- Yalçın Yaman
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey.
| | - Veysel Bay
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
- Aegean Agricultural Research Institute, Menemen, İzmir, Turkey
| | - Ramazan Aymaz
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
| | - Murat Keleş
- Department of Biometry and Genetics, Sheep Breeding and Research Institute, 10200, Bandırma, Balıkesir, Turkey
| | - Yasemin Öner
- Department of Biometry and Genetics, Agricultural Faculty, Bursa Uludag University, 16000, Bursa, Turkey
| | - Eden Yitna Teferedegn
- Armauer Hansen Research Institute, Biotechnology, and Bioinformatics Directorate, Addis Ababa, Ethiopia
- Department of Biology, Faculty of Science, Aegean University, 35000, İzmir, Turkey
| | - Cemal Ün
- Department of Biology, Faculty of Science, Aegean University, 35000, İzmir, Turkey
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5
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Bay V, Keleş M, Aymaz R, Hatipoğlu E, Öner Y, Yaman Y. Documentation of extensive genetic diversity in the Ovar- DRB1 gene in native Turkish sheep. Anim Biotechnol 2021; 32:507-518. [PMID: 33606604 DOI: 10.1080/10495398.2021.1884086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Indigenous breeds have a high level of genetic diversity that might contribute to develop animal breeds with desired traits such as disease resistance and high productivity. Major histocompatibility complex (MHC) is a key component of adaptive immune system and consists of highly polymorphic genes that take part in adaptive immune response and disease resistance. Exploring and understanding the effect of polymorphisms in MHC could be beneficial to future animal breeding strategies. In this study, we sequenced the highly polymorphic Exon2 of the ovine DRB1 gene using Sanger sequencing to explore the diversity of this gene in six indigenous Turkish sheep breeds and two crossbreeds. In total, 894 haplotypes from 447 sheep were investigated, and 69 different haplotypes including 27 novel ones were identified. Among the identified haplotypes there were common and breed specific haplotypes. There was a relatively high diversity of the alleles within indigenous breeds. Allelic diversity patterns were mostly associated with geographical differences. The results of this study highlight the genetic variation within indigenous breeds which has important implications for biodiversity and the adaptability of breeds to specific environments. There is value to further studies which include other genomic regions and traits, and these could guide breeding strategies.
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Affiliation(s)
- Veysel Bay
- Department of Biometrics and Genetics, Sheep Breeding and Research Institute, Bandirma, Balıkesir, Turkey
| | - Murat Keleş
- Department of Biometrics and Genetics, Sheep Breeding and Research Institute, Bandirma, Balıkesir, Turkey
| | - Ramazan Aymaz
- Department of Biometrics and Genetics, Sheep Breeding and Research Institute, Bandirma, Balıkesir, Turkey
| | - Ecem Hatipoğlu
- Department of Biometrics and Genetics, Sheep Breeding and Research Institute, Bandirma, Balıkesir, Turkey
| | - Yasemin Öner
- Department of Biometry and Genetics, Faculty of Agriculture, Uludağ University, Bursa, Turkey
| | - Yalçın Yaman
- Department of Biometrics and Genetics, Sheep Breeding and Research Institute, Bandirma, Balıkesir, Turkey
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MHC-DRB1 exon 2 polymorphism and its association with mycoplasma ovipneumonia resistance or susceptibility genotypes in sheep. J Genet 2020. [DOI: 10.1007/s12041-020-1175-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Semple SL, Dixon B. Salmonid Antibacterial Immunity: An Aquaculture Perspective. BIOLOGY 2020; 9:E331. [PMID: 33050557 PMCID: PMC7599743 DOI: 10.3390/biology9100331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 02/08/2023]
Abstract
The aquaculture industry is continuously threatened by infectious diseases, including those of bacterial origin. Regardless of the disease burden, aquaculture is already the main method for producing fish protein, having displaced capture fisheries. One attractive sector within this industry is the culture of salmonids, which are (a) uniquely under pressure due to overfishing and (b) the most valuable finfish per unit of weight. There are still knowledge gaps in the understanding of fish immunity, leading to vaccines that are not as effective as in terrestrial species, thus a common method to combat bacterial disease outbreaks is the use of antibiotics. Though effective, this method increases both the prevalence and risk of generating antibiotic-resistant bacteria. To facilitate vaccine design and/or alternative treatment efforts, a deeper understanding of the teleost immune system is essential. This review highlights the current state of teleost antibacterial immunity in the context of salmonid aquaculture. Additionally, the success of current techniques/methods used to combat bacterial diseases in salmonid aquaculture will be addressed. Filling the immunology knowledge gaps highlighted here will assist in reducing aquaculture losses in the future.
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Affiliation(s)
| | - Brian Dixon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
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Özdil F, İlhan F, Işık R. Genetic characterization of some Turkish sheep breeds based on the sequencing of the Ovar-DRB1 gene in the major histocompatibility complex (MHC) gene region. Arch Anim Breed 2018; 61:475-480. [PMID: 32175456 PMCID: PMC7065386 DOI: 10.5194/aab-61-475-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/22/2018] [Indexed: 12/03/2022] Open
Abstract
In this research, Ovar-DRB1 gene in the major histocompatibility complex (MHC) gene region was surveyed by
DNA sequencing in some of the native sheep breeds that are reared in Turkey.
A total of 80 samples were collected from eight different Turkish native sheep
breeds, and these samples were used for DNA sequencing. The exon 2 region of Ovar-DRB1 in the MHC gene region was polymerase chain reaction (PCR) amplified and sequenced. A
total of 25 new alleles were revealed in the Ovar-DRB1 gene in Turkish native sheep breeds
with 24 variable sites; only 13 sites were parsimony informative. The
average pairwise genetic distance was 0.029 % for the Ovar-DRB1 gene exon 2 region.
The sequence variations at eight different positions (7026, 7036, 7040, 7053,
7059, 7069, 7131 and 7214) are found in all of the studied samples. G →
C transversion at position 7081 is only seen in Akkaraman sheep breed,
whereas T → C transition at position 7097 is only seen in one sample
from the Akkaraman breed. Overall, two main groups were detected among the 25
alleles from Turkish native sheep breeds. All Daǧliç and Kivircik alleles
and one allele from Karayaka, Malya and Sakiz are grouped together while all
the other breeds are grouped in the other branch.
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Affiliation(s)
- Fulya Özdil
- Dept. of Agricultural Biotechnology, Namık Kemal University, Tekirdağ, Turkey
| | - Fatma İlhan
- Dept. of Animal Science, Selçuk University, Konya, Turkey
| | - Raziye Işık
- Dept. of Agricultural Biotechnology, Namık Kemal University, Tekirdağ, Turkey
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9
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Cinar MU, Mousel MR, Herrmann-Hoesing LM, Taylor JB, White SN. Ovar-DRB1 haplotypes *2001 and *0301 are associated with sheep growth and ewe lifetime prolificacy. Gene 2016; 595:187-192. [DOI: 10.1016/j.gene.2016.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/15/2016] [Accepted: 10/01/2016] [Indexed: 01/26/2023]
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10
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Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea. Genes (Basel) 2016; 7:genes7070036. [PMID: 27429004 PMCID: PMC4962006 DOI: 10.3390/genes7070036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 11/16/2022] Open
Abstract
The swine leukocyte antigens (SLAs) are the multigene families related to immune responses. Little is known about the effect of the DRA gene on diarrheal disease. This study reported the genetic diversity of the DRA gene in exons 1, 3 and 4 in 290 Chinese Yantai black pigs. No variation was identified in exon 3. In exon 1, three genotypes and two alleles were identified, generated by two single nucleotide polymorphisms (SNPs). In exon 4, there were eight genotypes and five alleles containing seven SNPs were detected with four SNPs being novel SNPs. The low polymorphism found in swine DRA is consistent with the concept that the DRA gene is highly conserved among all mammalian species. Statistical analyses indicated that the genotypes of exon 1 were not significantly associated with piglet diarrhea (p > 0.05); however, genotypes C₄C₄ (1.80 ± 0.33) and A₄E₄ (1.66 ± 0.25) of exon 4 were significantly susceptible to diarrhea (p < 0.01). These indicate that the particular genotypes of the DRA gene are susceptible to diarrheal disease, which provides valuable information for disease-resistance breeding in swine.
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11
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Pokorska J, Kułaj D, Dusza M, Żychlińska-Buczek J, Makulska J. New Rapid Method of DNA Isolation from Milk Somatic Cells. Anim Biotechnol 2016; 27:113-7. [PMID: 26913552 PMCID: PMC4806335 DOI: 10.1080/10495398.2015.1116446] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Isolation of genomic DNA is one of the basic steps in many different molecular analyses. There are a few reports on methods of DNA isolation from milk, but many of them are time consuming and expensive, and require relatively large volumes of raw milk. In this study a rapid, sensitive, and efficient method of DNA extraction from milk somatic cells of various mammals (cattle, sheep, goats, horses) is presented. It was found that milk is a good source of genomic DNA, and to obtain a sufficient amount and quality of DNA, suitable for molecular analysis such as PCR, 10 mL of raw milk is sufficient. Thanks to this method, stress in animals can be reduced during collection of researched material. Therefore, this method could be widely used in molecular analyses.
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Affiliation(s)
- Joanna Pokorska
- Department of Cattle Breeding, University of Agriculture in Krakow, Institute of Animal Science, Krakow, Poland
| | - Dominika Kułaj
- Department of Cattle Breeding, University of Agriculture in Krakow, Institute of Animal Science, Krakow, Poland
| | - Magdalena Dusza
- Department of Cattle Breeding, University of Agriculture in Krakow, Institute of Animal Science, Krakow, Poland
| | - Justyna Żychlińska-Buczek
- Department of Cattle Breeding, University of Agriculture in Krakow, Institute of Animal Science, Krakow, Poland
| | - Joanna Makulska
- Department of Cattle Breeding, University of Agriculture in Krakow, Institute of Animal Science, Krakow, Poland
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Liu LX, Zhao SG, Lu HN, Yang QL, Huang XY, Gun SB. Association between polymorphisms of the swine MHC-DQA gene and diarrhoea in three Chinese native piglets. Int J Immunogenet 2015; 42:208-16. [PMID: 25736511 DOI: 10.1111/iji.12186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 12/30/2014] [Accepted: 02/02/2015] [Indexed: 12/26/2022]
Abstract
Swine leucocyte antigen (SLA) is a highly polymorphic multigene family that plays a crucial role in swine immune response and disease resistance. Here, we identified polymorphisms and gene variations of SLA-DQA exon 2 using polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing analysis, and further investigated the correlation between the polymorphisms and piglet diarrhoea in three Chinese native pig breeds (Bamei, Juema and Gansu Black pigs). Consequently, 12 genotypes and 8 alleles including two novel alleles were detected. Nucleotide polymorphism was compared with the actual functional polymorphism in the peptide-binding region (PBR), binding pockets P1, P6 and P9, and the antigen-binding groove, variations in the antigen-binding groove of alleles DQA*01xa01, DQA*01xa03, DQA*01xb01, DQA*We02, DQA*03xb03 and DQA*wy06 were higher than alleles DQA*03xa01 and DQA*03xa03, while amino acid variations in peptide-binding pockets of allele DQA*03xa03 were most abundant among all alleles. The results of association analysis showed the diarrhoea score of Gansu Black pigs (-0.08 ± 0.78) was significantly higher than Bamei and Juema pigs (P < 0.01), and genotype DQA*03xa0103xa01 (0.39 ± 0.54) was significantly higher relative to other genotypes (P < 0.01), while that of genotype DQA*03xa0303xa03 (-1.31 ± 0.88) was markedly lower than scores obtained with genotypes DQA*03xa0103xa01 and DQA*03xa0101xa01 (P < 0.01), as well as DQA*01xa0101xa01 (P < 0.05), indicating that amino acid variations in the peptide-binding pockets play a more important role than the antigen-binding groove in piglet diarrhoea resistance. Further studies on other SLA molecules of native pigs are required to validate the link between this gene complex and diarrhoea.
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Affiliation(s)
- L X Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,College of Life Science and Engineering, Northwest University for Nationalities, Lanzhou, China
| | - S G Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - H N Lu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,College of Life Science and Engineering, Northwest University for Nationalities, Lanzhou, China
| | - Q L Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - X Y Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - S B Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, China
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